The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies

Abstract

The introduction of third-generation DNA sequencing technologies in recent years has allowed scientists to generate dramatically longer sequence reads, which when used in whole-genome sequencing projects have yielded better repeat resolution and far more contiguous genome assemblies. While the promise of better contiguity has held true, the relatively high error rate of long reads, averaging 8-15%, has made it challenging to generate a highly accurate final sequence. Current long-read sequencing technologies display a tendency toward systematic errors, in particular in homopolymer regions, which present additional challenges. A cost-effective strategy to generate highly contiguous assemblies with a very low overall error rate is to combine long reads with low-cost short-read data, which currently have an error rate below 0.5%. This hybrid strategy can be pursued either by incorporating the short-read data into the early phase of assembly, during the read correction step, or by using short reads to "polish" the consensus built from long reads. In this report, we present the assembly polishing tool POLCA (POLishing by Calling Alternatives) and compare its performance with two other popular polishing programs, Pilon and Racon. We show that on simulated data POLCA is more accurate than Pilon, and comparable in accuracy to Racon. On real data, all three programs show similar performance, but POLCA is consistently much faster than either of the other polishing programs.

References 14

1. 1.

   This reference’s wording can’t be shown under the paper’s licence.

   Not in our library

2. 2.

   This reference’s wording can’t be shown under the paper’s licence.

   Not in our library

3. 3.

   This reference’s wording can’t be shown under the paper’s licence.

   Not in our library

4. 4.

   This reference’s wording can’t be shown under the paper’s licence.

   Not in our library

5. 5.
   Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement · 2014

   No notice
6. 6.

   This reference’s wording can’t be shown under the paper’s licence.

   Not in our library

7. 7.

   This reference’s wording can’t be shown under the paper’s licence.

   Not in our library

8. 8.

   This reference’s wording can’t be shown under the paper’s licence.

   Not in our library

9. 9.

   This reference’s wording can’t be shown under the paper’s licence.

   Not in our library

10. 10.
    MUMmer4: A fast and versatile genome alignment system · 2018

    No notice
11. 11.
    Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation · 2017

    No notice
12. 12.
    Completing bacterial genome assemblies with multiplex MinION sequencing · 2017

    No notice
13. 13.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

14. 14.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

Cited by papers we hold 4

• Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing · 2023
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• First Report of Chromosome-Level Genome Assembly for Flathead Grey Mullet, Mugil cephalus (Linnaeus, 1758) · 2022
  Not checked
• Polypolish: Short-read polishing of long-read bacterial genome assemblies · 2022
  No notice
• Accurate long-read de novo assembly evaluation with Inspector · 2021
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